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Related Concept Videos

Modern Molecular Taxonomy01:29

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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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Wochenende - modular and flexible alignment-based shotgun metagenome analysis.

Ilona Rosenboom1, Tobias Scheithauer2, Fabian C Friedrich2

  • 1Clinical Research Group Molecular Pathology of Cystic Fibrosis and Pseudomonas Genomics, Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany. rosenboom.ilona@mh-hannover.de.

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Summary

Wochenende is a new pipeline for shotgun metagenome analysis that improves accuracy by filtering alignments and provides transparent results. It visualizes microbial communities and calculates growth rates for all life kingdoms.

Keywords:
Absolute quantificationGenomicsLong-read metagenomicsMetagenomic visualizationMetagenomics

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Shotgun metagenome analysis is crucial for microbiome studies.
  • Existing tools lack standardized output and clear mapping information.
  • Accurate mapping visualization is essential for reliable results.

Purpose of the Study:

  • To develop a robust and transparent pipeline for metagenome analysis.
  • To improve the accuracy of taxonomic classification and functional gene analysis.
  • To provide tools for visualization and growth rate calculation.

Main Methods:

  • Developed the Wochenende alignment-based pipeline.
  • Incorporated flexible quality control, trimming, mapping, and filtering.
  • Implemented novel normalization for absolute abundance profiling.

Main Results:

  • Wochenende reduces false positives through stringent filtering.
  • Provides transparent, user-adjustable results and genomic visualization.
  • Enables calculation of growth rates and absolute abundance profiles.

Conclusions:

  • Wochenende analyzes all kingdoms of life using short and long reads.
  • The pipeline integrates quality control, normalization, and taxonomic visualization.
  • Wochenende is publicly available for research use.